7 Jan

January 17th, 2024 – Guest Speaker: Hannes Klump

Mark your calendar! On January 17th, 2024, Hannes Klump, Director of Transfusion Medicine and Cell Therapeutics at the Uniklinik RWTH Aachen, will talk about

The quest for novel HOX-gene combinations promoting hematopoietic stem cell development from (i)PSCs.

Induced pluripotent stem (iPS-) cells may become a promising source for the generation of patient-specific hematopoietic stem cells (HSCs), in vitro. However, protocols allowing for the directed, efficient generation of HSCs with long-term multilineage repopulating properties do not exist yet. So far, the most robust strategy for generating hematopoietic progenitors from pluripotent cells, in vitro, has been established in the mouse model involving ectopic expression of the human transcription factor HOXB4, as we have repeatedly shown. Its enforced expression promotes the formation of hemogenic endothelium cells and their subsequent morphologic transition to early hematopoietic progenitors. Nevertheless, it is not sufficient to mediate a complete, final maturation to an adult phenotype comparable to bone-marrow resident HSCs, in vitro. Because of the paramount role of HOX-genes for development and maintenance of HSCs, one the aims of our lab is to identify combinations which allow for the de novo generation of fully mature HSPCs from differentiating mouse and human PSCs and, also, the expansion of adult HSPCs.

Join us for insights into exciting science on January 17th, 3 p.m., at the University Hospital Regensburg KUNO (Buildiung C5), room 3.552!

13 Dec

Comment on the 2023 Nobel Prize

The 2023 Nobel Prize in Physiology or Medicine has been awarded to Katalin Karikó and Drew Weissman for their breakthrough discoveries to use modified RNA for therapeutic treatments. Together with Herbert Tschochner, we have written a short comment to celebrate the occasion. We highlight the importance of the discoveries made by Katalin Karikó and Drew Weissman and how they have contributed to the development of RNA-based therapies. The comment can be accessed at Pflugers Archiv – European Journal of Physiology via this link.

17 Jul

New publication: Investigating the Prevalence of RNA-Binding Metabolic Enzymes in E. coli

RNA interactome studies suggested that numerous metabolic enzymes possess the ability to bind RNA. This has fueled the REM hypothesis that describes the regulatory interplay of RNAs, metabolic enzymes and metabolites. In a collaborative effort, a consortium comprising the Meister, Suess, and Rossbach labs and headed by the Babinger lab, has investigated RNA binding of select enzymes in E.coli using iCLIP, SELEX, MST, and EMSA experiments. This revealed specific RNA interaction of glutamate-5-kinase (ProB) and quinone oxidoreductase (QorA). It will be exciting to learn about the functional consequences and the biological importance of these protein RNA interactions. The open-access publication can be found here: weblink.

12 Jul

New publication from the lab: Ribosome Profiling in the Model Diatom Thalassiosira pseudonana

In a close collaboration with Monica Pichler from the lab of Thomas Mock at at he University of East Anglia, we could establish ribosome profiling for the Diatom Thalassiosira pseudonana. This unicellular organism belongs to an important group of eukaryotic microalgea that play a key role as primary producers in aquatic ecosystems, generating 20-50% of the oxygen on the planet each year, and comprising approx. half of the organic material found in the oceans. With ribosome profiling now available for diatoms, it can now be determined how changing environmental conditions such as acidification of the oceans or an increase in water temperature affect protein synthesis in the model organism T.pseudonana. Please find the open access publication at Current Protocols: weblink.

29 Jun

New publication from the lab: High resolution and rapid ribosome profiling from low-input samples

Our protocol for rapid ribosome profiling of small input samples has been published in Nucleic Acids Research. We demonstrate the outstanding performance of the newly developed sequencing library preparation workflow and its reproducibility with minute amounts of sample (0.1 pmol of RNA). We would like to thank our collaborators (Meister lab at the University of Regensburg, Leidel lab at the University of Bern & König lab at IMB Mainz) for their support! Please find the open access publication here: weblink.

25 Nov

New preprint from the lab

Are you interested in establishing ribosome profiling in your lab to analyze cellular translation comprehensively and quantitatively?

Check out our novel and simplified protocol! The standardized workflow employs an extremely rapid sequencing library preparation protocol (12 hours) that relies on solid phase extraction of reaction intermediates, making it easy to implement in any standard laboratory. The protocol yields data of extremely high quality from minute amounts input material allowing the analysis of samples that were previously not easily amenable to this type of experimentation.

Access the preprint on bioRxiv here

If you are interested in practical training on how to perform the experiments, make sure to apply for a spot in the EMBO Practical Course on Measuring translational dynamics by ribosome profiling (March 26 – April 1 2023 at EMBL Heidelberg)

10 Jul

EMBO Pratcial Course

We are very happy to announce that our funding application for a second round of the EMBO Practical Course Measuring translational dynamics by ribosome profiling has been successful!

On behalf of all organizers, I would like to thank the expert speakers that have agreed to support the course: Nicholas Ingolia, Rachel Green, Anne Willis, Marina Rodnina, Noam Stern-Ginossar, Michael VanInsberghe, and Vladimir Benes.

The course will take place from March 26th to April 1st at the Advanced Training Centre (ATC) at the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany. We are very much looking forward to your applications and a week packed full of exciting science and labwork! Stay tuned and/or check the official webpage for updates and details.

6 Jun

New publication: Molecular insights into Mei-P26 function

Our study of the activity of tha TRIM-NHL protein Mei-P26, a regulator of cell fate in Drosophila, has now been published at Life Science Alliance (doi 10.26508/lsa.202201418).

In a close collaboration with the labs of Sebastian Glatt (Max Planck Research Group at the Malopolska Centre of Biotechnology, Jagiellonian University Krakow, Poland) and Janusz Bujnicki (Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Poland), we could solve the first high resolution structure of the Mei-P26 NHL domain and define a consensus RNA motif that it recognizes. Molecular dynamics simulations allowed us to predict and subsequently experimentally validate key amino acid residues involved specific RNA recognition, highlighting differences to other NHL domains. Using individual nucleotide resolution cross-linking and immunoprecipitation (iCLIP), we could identify RNA targets of Mei-P26 in cultured Drosophila cells and demonstrate the protein can either repress or activate its genuine mRNA targets. Regulation requires the NHL domain of the protein but is independent of its function as a ubiquitin ligase.

In particular, the last finding significantly expands our understanding of TRIM-NHL protein-mediated gene regulation. These proteins were previously considered to exclusively act as repressors of gene expression. Strikingly, Mei-P26 itself appears to lack any regulatory activity suggesting that the regulatory outcome is determined by the recruitment of different co-factors, some of which have previously been identified.

29 Apr

Ribosome Profiling Course

We had an exciting time during the practical course on rapid and high sensitivity analyses of cellular translation by ribosome profiling. 13 international participants joined us in Regensburg for a five day lab course during which they very successfully prepared ribsome profiling libraries from a human cell line using only minute amounts of input material.

We would like to thank all participants for their enthusiasm and for sharing with us insight into their exciting research projects! We had a great time working together and discussion science with you.

We also thank Sebastian Leidel (Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Switzerland) and Thomas Preiss (John Curtin School of Medical Research at the Australia National University, Australia) for supporting the course with exciting lectures and for contributing expert opinions and insight into the challenges and pitfalls of performing ribosome profiling experiments.

We are grateful for the support by the Graduate Research Academy RNA Biology of the Collaborative Research Center SFB 960 and siTOOLs Biotech.

30 Mar

Course News

Dear participants, please find some information on the practical course on ribosome profiling here. The information will be frequently updated… Looking forward to meeting you in Regensburg!

7 Feb

Practical course on ribosome profiling

I would like to bring to your attention the following practical course which we will host in Regensburg from April 25th to 29th: 2022:

Practical course on rapid and high-sensitivity analyses of cellular translation by ribosome profiling

This hands-on course will teach how to generate comprehensive and quantitative snapshots of cellular translation from minute amounts of sample. Starting from cultured cells, ribosome-protected fragments will be produced, purified, and subjected to sequencing library preparation using a streamlined protocol which is optimized for small amounts of input. Detailed background information will be provided on (1) the optimization and adaptation of ribosome profiling to different model systems and research questions, (2) state-of-the-art sequencing library preparation, and (3) the bioinformatic analyses of ribosome profiling data.

Guest speakers will be: Sebastian Leidel (Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Switzerland) and Thomas Preiss (John Curtin School of Medical Research at the Australia National University, Australia)

Apply by March 27th with your CV and a letter of motivation to info@rnabiology-regensburg.de. There are no registration fees!

This course is supported by the graduate school of the Graduate School RNA Biology of the Collaborative Research Centre 960 (SFB960) – RNP biogenesis: assembly of ribosomes and non-ribosomal RNPs and control of their function

2 Feb

Pressemitteilung zum Weltkrebstag

Pünktlich zum Weltkrebstag, dem 04. Februar, erscheint eine Pressemitteilung über unsere Forschungsergebnisse. Gemeinsam mit unseren Partnern Robert Ahrends, Grischa Tödt, Björn Tews und Christiane Knobbe-Thomsen, haben wir einen neuen Mechanismus entdeckt, der in Tumorzellen eine Resistenz gegen weit verbreitete Chemotherapeutika auslöst. Diese Chemoresistenz hat dramatische Folgen für betroffene Patienten, da die Behandlung stark eingeschränkt wird. Ein besseres Verständnis des Mechanismus der Chemoresistenz soll zukünftig neue Therapieoptionen ermöglichen.

Gefördert wurde die Forschungsarbeit im SUPR-G (Systems Biology of the Unfolded Protein Response in Glioma) Konsortium durch das Bundesministerium für Bildung und Forschung (BMBF) im Rahmen der e:med Initiative (Maßnahmen zur Etablierung der Systemmedizin).

21 Dec

Ribosome Profiling Practical Course

From January 17th to 21st, we will run a practical course on ribosome profiling at the Justus-Liebig-University in Gießen. Focusing on our newly-developed and high-sensitivity protocol, we will teach students of the DFG-funded Research Training Group 2355 ‘Regulatory networks in the mRNA life cycle: from coding to non-coding RNAs’ how to analyze cellular translation using ribosome profiling. We are very much looking forward to the course and to introducing our ultra-rapid protocol to our colleagues for the first time.